The present invention discloses a method for heat treatment of hypereutectoid steel rail, including the following steps: holding the temperature of the steel rail of which temperature is above 900° C. after finish rolling, conducting a first cooling stage for the steel rail at the first cooling speed after the temperature holding to reduce the temperature of railhead surface layer of the steel rail to 700-750° C., conducting a second cooling stage for the steel rail at the second cooling speed to reduce the temperature of railhead surface layer of the steel rail to 550° C., conducting a third cooling stage for the steel rail at the third cooling speed to reduce the temperature of railhead surface layer of the steel rail to 450° C. or less, and continuing to cool the steel rail in the air. While obtaining good tensile property, the steel rail treated by the method for heat treatment provided by the present invention can effectively reduce secondary cementite and have excellent resistance to abrasion and contact fatigue. The product is particularly suitable for heavy rails.